Leaving is the Hardest Thing I had to do!
by thephoenixsong
Summary: Elizabeth is leaving Atlantis. John doesn't want her to leave, she gets mad, they stop talking until the night before she leaves. They don't enough time to spend with each other. They have a plan to get Elizabeth back to Atlantis. Set before season 4.


Author: Louise Mills

Rating: **M**

Authors Note: Just something that came to me at work and I had to type it on the computer. Has no spoiler's of season three. I'm not good with writing English (even though I am English, but that's things go sometimes.) But I have got better since I first started writing. So please excuse my grammar and spelling etc.

Disclaimer: I don't owe anything related to the programme Stargate Atlantis or it's characters.

_**Leaving is the Hardest Thing I had to do! **_

"You're leaving?" John questioned Elizabeth. Astounded he was only finding out now and that she hadn't discussed it with him about putting in her resignation, after all he consider her his best friend, maybe he suddenly realise he was the only one to think that.

"Yes." She simply replied. She knew John would be upset and I hoped she had a few more days until he founded out.

"Why? You love Atlantis!" He stated, his mind working in overdrive. "They're forcing you out!" He stressed. It was the only conclusion his mind came up with.

"No, it was my choice and how did you find out so quickly?" She questioned, hoping he didn't see she had lied. She knew if she didn't resigned, they would have forced her out, she just didn't feel like fighting any more.

"General O'Neill just informed me and don't change the subject, of course they're behind your decision." He yelled.

"John they weren't, it was my decision!" She stressed loudly. Trying to make him believe.

"Then I question again, why would you want to leave Atlantis?" He hoped he could trick her into saying it was really the IOA's decision.

"I don't have to explained myself to you Colonel!" She yelled back, realising what he was trying to do. John stepped back in surprise, he didn't realised he had provoked her so much, especially to the point to make her start to yell and in a cold tone. Silence penetrated the room, John not knowing what to say and Elizabeth silently fuming in angry all directed at John and not really knowing why, as it wasn't his fought she was leaving, he was just the first person to see after putting in her resignation.

Getting more irritated by John's presence, she needed him gone, so she prepared to say something she never wanted to say to him, since they started their conversion.

"If you don't have anything to report or something else to talk about other then my pending departure, you are dismissed Colonel!" She spoke in a steady harsh cold voice. She saw a flicker of hurt flash in his eyes, before it was quickly masked over. 'Always the military Colonel, never just a man' Elizabeth thought.

John straightens his back and rolled his shoulders, he had never expected her to talk to him in such a manner or tone, for no reason. In that instant he knew he was saying goodbye to his closest friend 'Elizabeth' and saying hello to Dr Weir the strong leader.

He turned and marched to the door, he had his hand on the door release and he momentary paused, believing he should say something to at least fix their friendship, but he quickly squashed the idea, after all she should be doing the fixing, she broke it. He waved his hand over the door release and marched out of the control tower, leaving a stunned Elizabeth in her office.

He stepped into the transporter and waited for the doors to close, he then leaned back and closed his eyes.

"Goodbye Elizabeth." He whispered, once the words had passed over his lips, his whole chest ached with a pain, he never once remembered having before. After a few more the minutes and the pain hadn't lessen, he managed to composed himself, he hadn't realise it would hurt so much to let her go. Finally after a few minutes he managed to touch the screen on the transporter to where he wanted to go.

She thought he would say something before he left, but all she got was silence, dread finally filled every part of body.

"What have I done?" She questioned herself in a whisper. She had only wanted him to leave, she didn't want to damage their friendship, which she had a feeling she had just done. She hoped he was only angry and once he had cooled down he would talk to her again.

As the weeks passed the time of her pending departure was nearing, she came to the conclusion she had damaged her and John's friendship beyond repair, for the last two weeks since she shouted at him and dismissed him, John had only spoke to her when was required. Meaning only when she wanted a military opinion, him suddenly coming all professional had hurt, but she realised she had placed the hurt on herself and she will just have to live with it.

She was only glad he didn't ran straight to his team after she dismissed him two weeks ago and let herself tell the people of Atlantis that she was leaving and they should expect her replacement a week before she left, she joked saying 'to show them the ropes'. Surprise was the order for that day, a week ago, now she only had one more day until her replacement would arrive, she had no idea whom the IOA had chosen, she god damn wasn't going to befriend her replacement, once they arrive she would stay with them the first full day to show how she ran the place and after that, she would only stay to help when necessary, after all she had a lot of things to pack.

SGA-1 was sitting in the mess silently wondering what Elizabeth's replacement was going to be like, expect for John as he had just realised he was in love with Elizabeth. He still ached for her and it hurt more when he was in her presence; when he first came here he never expected to full in love, especially not with his boss. He knew she only had one week until she left him for good and that hurt more then he thought possible, if she wasn't leaving and he found out he loved her, he would tell her, but now he had decided to stay quiet, after all what's the point of telling her, she would still be leaving. Him telling her wouldn't get her to stay, so why cause himself more pain, was his reasoning. He was drawn out of his thoughts when he realised Rodney had asked him a question.

"Sorry Rodney, what were you saying?" He asked, a low voice. He knew he sounded down, but he just couldn't put the energy in anything he did any more, to make people believe he was okay. Teyla frowned and she noticed Ronan doing the same, they both looked at each other and could tell they were both wondering what was wrong with him, only Rodney didn't seem to hold back in assessing John.

"What the hell is wrong with you? You are acting like someone had killed your favourite puppy dog!" Rodney stated without thought. John breathed in the calming breath he didn't need the fly of the rails at Rodney, what he need all of his friends at the moment and that did include Rodney.

"Nothing's wrong Rodney, I just got out of the wrong side of bed today." He replied hoping it would throw the inquisitive scientist off from him. Teyla and Ronan realised then that John didn't want the talk about what was really bothering him, as they all knew John had just lied. Rodney obviously didn't seem to get the memo that said, it leave everything alone.

"What the hell! Does that mean you have got out of the wrong side of bed for the last two weeks? Because that's how long you have been in this miserable state and I'm getting sick and tried of seeing a down in the dumps Sheppard, buck up already! So the answer to my question, why do you think Elizabeth is leaving and why didn't she fight for her position?" Rodney questioned, unaware that John physical leaned back, let out a big sigh and closed his eyes. Teyla glanced meaningful to Ronan; her glance stated Elizabeth was the reason for John being slightly depression. Ronan only nodded back.

"Rodney I say this once and only once, I have no idea why Elizabeth so freely gave up for position and why she didn't fight. I can tell you now at this moment in time I really don't care!" John steady calm voice turn cold as he spoke. Which shocked the rest of his team, they had never heard John talk about Elizabeth that way and especially in that tone. John stood up taking his tray with him.

"See you guys later!" He muttered as he left.

"What the hell is going on?" Rodney exclaimed loudly.

"I do not know Rodney, but I think we should give him space, I will try and talk to him later when we spar." Teyla said in her normal calming voice.

"Oh okay, you will tell me if you found anything out?" He questioned, he was more worried for John then he hoped he had projected.

"Of course Rodney, if I believe you have a right." She answered knowing all to well how much Rodney worried for the team leader.

"Right, okay I have work to do, meet you both later?" He asked.

"Sure McKay!" Ronan answered. Once Rodney got his answer he stood up himself and left the mess.

"Well there is obviously something wrong with John and Elizabeth's Relationship." Ronan stated.

"Yes, and I intend to find found out what." Teyla reply.

Teyla landed hard on the sparring floor after John and managed to successful flip her over, after doing a clean attack set. Teyla rubbed her hand over her hip, she hadn't expected John to go for that move, so hadn't prepared herself with the out come in case he successful pulled it off, which he had, which was causing her pain now.

"You have been practising." She stated while getting up and sitting down on the bench.

"Believe it or not, I haven't." He stated. Not even enquiring if she was okay, which was his usual banter when they sparred and he won the set.

"What's wrong John?" She asked, thinking he seem okay now to asked the question she desperately wanted an answer for. John, whose back had been facing her, quickly turn around and marched up to her. Which slightly scared her, because of the haunting look in his eyes.

"Why is everyone all the sudden concern and asking me if I'm okay? I fine!" He growled at her.

"No you are not! If you can't see there is something wrong, maybe I should ask Elizabeth, maybe she will know what's wrong." Once she finished what she was saying she realised she should never had said anything about Elizabeth, as that's then his eyes turn from fierce angry to withdrawn cold stone.

"Don't go there, Teyla, I know what you really want to know, but you get me saying anything, if you want to know, ASK ELIZABETH." He Growled and shouted at Teyla. John rushed out of the room and ran to his quarters, he didn't know why everyone couldn't just leave everything alone; he just wanted to be left alone.

Tomorrow he will have to face the person that was replacing Elizabeth and he wasn't happy about that, he just wished she fought for herself, like the Elizabeth he loved would have done, he knew in the end they would have still replaced her, but he wanted his Elizabeth back. The one full of life not the one that gave up before anything happen, because that is want she did gave up and he didn't like it.

He was more disappointed that she didn't try and fight for their friendship, then with her being replaced now. After a week when they had their argument she had told the rest of Atlantis what was happening and still hadn't even approached him to try and fix their friendship, it hurt more then the words she said to him two weeks ago.

They say actions speak louder then words and her actions spoke that she didn't want him in her life, when he realised that a few days ago it broke his heart and he hasn't really been the same since and everyone was starting to notice. But how do you mend a broke heart? He thought sitting alone in his dark room.

Elizabeth was packed and ready to go, but she still had one more day until is left Atlantis possibly forever. She thought about her time here and the one constant she had in the last 3 years, expect for the last three weeks was, John. Earlier she had heard Teyla speaking with Ronan and Rodney in the mess, she was surprised John wasn't with them, as they never seem to be apart when it came to meal.

What she heard she didn't think is would forget.

_**Flashback**_

"So have you spoken to him again?" She heard Rodney say in an expectation voice.

"Yes and he won't speak about it. He keeps saying he is fine." She heard the unique voice of Teyla response.

Wondering whom they were talking about Elizabeth turned around; making sure none of them would see her.

"It's is getting beyond a joke!" Rodney exclaimed.

"Obvious he doesn't want us to interfere maybe we should respect his wishes." Ronan stated.

"Come one this is Sheppard we are talking about!" Rodney replied.

"Yes and he is entitled to his privacy." Teyla answered.

"Okay!" Rodney replied, bring up his hands in 'I give up' pose. "But you must have a idea what is wrong with him?" Rodney question quietly. Quiet enough that Elizabeth almost didn't hear him and she was really interested in the conversion. She had noticed John hadn't been himself recently and was concerned.

"Well, I believe Elizabeth and John's Friendship has broken down and he is having a hard time dealing with it." Teyla stated plainly. Elizabeth startled she knew it could you been that reason, but she never expect him to be so affected by the break down.

"Then why hasn't he done anything about it? I can't image them two not getting along." Rodney stressed.

"He didn't exactly say but I believe he thinks it's all Elizabeth's fought and so that she should make the first move. Which probably means she hasn't made the first move, because his still…" Teyla said. She filtered off, not knowing how to descried the way John has been acting.

"Depressed, down in the dumps, acting like a love sick teenager." Rodney finished for Teyla. All three of them paused to think while the impact of Rodney's last statement. Elizabeth stood up not needing to hear any more of their conversion, 'he wasn't talking to her, because he believed she should of made the first move, oh my god, I was so stupid. I attacked him with my best weapon, words, but still expected him to repair what I ruined' Elizabeth thought as she left the mess. Just she was going though the doors, she heard Rodney say one last thing.

"His in love with her!" He stated astounded.

_**End of Flashback**_

Now she had one more thing to do before she could leave Atlantis with a clear conscience and that was to talk to John. She wasn't looking forward to the conversion, because if Teyla, Ronan and Rodney were right she had hurt him, far more then she had realised. Her doing nothing for the past three weeks, could of made it now impossible to mend what she had done to their relationship.

She had been standing outside John's door for the last 30 minutes, pacing and playing with her hands in a nervous fashion trying to get the courage to knock on his door.

"God why this is so hard?" She questioned herself. Not realising the door had opened seconds before she ask herself the question.

"Because doing the right thing sometimes is the hardest thing we will have to do." John answered. Which made Elizabeth jump and quickly turned towards him. He was leaning on his doorframe and all she could think about was 'he looked like hell'. John was getting tiresome with yet another silence between them; he just had to break the silence even if it meant she would yell at him.

"What are you doing here Elizabeth?" He asked. Elizabeth was expecting him to be hostile; she was surprised when he wasn't.

"John, we need to talk. Can I come in?" Elizabeth asked, as she slowly walked closer. He nodded his head and let her in his room.

John sat down on his bed and gestured to Elizabeth to take a seat on one of the chairs. Silence fell, Elizabeth didn't know how to start the conversion and John just waited patiently. John felt a little hope, he hoped she had come here to fix at least their friendship.

"I'm sorry." Elizabeth uttered silently, but sounded louder in the quiet room. John of course knew what she was apologising for and wasn't going to pretend that he didn't, that would just make her angry.

John thought about her apology for a few minutes, Elizabeth was feeling anxious, but she was glad he was thinking about it. Of course is was slightly disappointed when he didn't quick jump in and forgiven her, a few years ago he would have just forgiven without thought.

"Elizabeth I forgive you, but why did it take so long to apologise?" He answered.

"Because I thought you didn't want to talk to me and in the past you were always the one to break the silence after we had an argument. When you didn't I thought you didn't want to know me any more." She replied. John couldn't believe what he was hearing and couldn't help but chuckle.

"Well, I usually broke to silence first, because I was the one that caused the problem, but I suppose I can understand why you would think I would break the silence first, after all you never needn't to before. I'm just very sad we didn't have this conversion weeks ago, you're going tomorrow." He stated, feeling low by the end of his statement. Elizabeth got up from the chair she was sitting on and walked over to John and sat next to him, grabbing his hand in hers.

"So I am!" She whispered. "Will you see me off tomorrow?" She questioned. John was stunned she would think he wouldn't; after all they had sorted out what was wrong with their relationship.

"Of course I'll be there!" He exclaimed. Silence descended again, but this time it was a comfortable silence. After a while John couldn't stand it any more and surprised Elizabeth then he quickly turned to face her and gathered her into his arms, hugging her like tomorrow was going to be the end of the world.

"God, I'm going to really miss you!" He whispered in her ear. He had no intention to let go and hoped she didn't pull away.

"Me too." She replied. She pulled him tighter letting him know she wasn't going to let go. After ten minutes of hugging each other their tight hold lessen. John laid down pulling Elizabeth with him; She got comfortable by lying her head on his chest.

"This is usually the point McKay comes and interrupts, that man has no sense of timing." John muttered looking at the door. Causing Elizabeth to laugh.

"Just don't open the door." She answered.

"I would if it was anyone other then McKay, you see he would just override the door and let himself in."

"He wouldn't… what if you had…um…company?" She question diplomatically. John chuckled.

"Because I wouldn't have company Elizabeth, the only company I would consider was…you." John answered. He was afraid what she thought about what he just said. She smiled at his statement; 'So the conversion his team had in the mess was true' She thought. Her thoughts just excited her more.

"Well that's good!" She replied playing with him. She realise he would think she was talking about the 'I wouldn't have company statement'.

"Elizabeth don't you realise what I'm trying to say to you?" He questioned.

"Of course I do."

"When pray tell me what you thought I said?" He questioned. Believing he would know her answer.

"That…you wouldn't need or want anyone else for your company, but me…because you…are…in…love…with…me." She answered with a smile. As said the words slowly and accented them, so he wouldn't get the wrong idea. John was stunned; he didn't expect her to state the truth.

"Well I suppose you do know what I was trying to say, god you didn't have to play with my feelings and you have…" John mumbled. He stopped then Elizabeth interrupted him with a kiss, shocking him. When she pulled away he still had his eyes closed, still stunned about the kiss. Once he had opened his eyes, he looked right back into her eyes.

"Does that mean you feel the same?"

"Yes John." She answered, before kissing him again. This time John kissed her back. Suddenly John's door chimed. John pulled away from Elizabeth and shoot off of bed.

"That man, defiantly has no sense in timing." He grumbled. He marched towards to his door, causing Elizabeth to chuckle. Just before he was going to open the door, he quickly turned towards Elizabeth.

"Do you want to hide or let him see you?" He questioned Elizabeth. Making sure she knew she had a choice and he wasn't ordering her round.

"I'm fine right where I am." She answered, which made John grin like a Cheshire cat. He turned to the door and it opened, he leaned on the door jam, meeting the one person he knew it was going to be.

"McKay, what do you want?" He asked. Rodney just looked at him weirdly.

"Are you feeling okay?" He asked in return.

"Yes McKay I'm." He sighed.

"That's what I mean, you seem okay. It's the total opposite to the way you have been acting lately." Rodney mumbled back.

"Is there a reason for your visit?" John questioned again.

"I'm looking for Elizabeth, you haven't seen her have you?" He questioned. Only then did Rodney look pass him into the room and saw the person he was looking for sitting on the bed, smirking. Rodney quickly looked towards John and saw he was also wearing a smirk.

"Yes Rodney?" Elizabeth asked, gesturing for both of them to come in, before they started a scene. Then he got closer the Elizabeth, Rodney noticed her hair was a little bit raffled, he suddenly realised he had interrupted them. He only cared for a moment, as he was on a mission, he had to get Elizabeth to the mess without her realising they were throwing her a party.

"So you are here why?" John asked, harshly and sat down on the bed next to Elizabeth. He want to get him out and spend the rest of his evening with Elizabeth, the only night they had left. He felt a bit depression when he realised they only had one night, when I could have had weeks.

"There's been an emergency we need Elizabeth." Rodney answered.

"Rodney, I'm no longer commander of the expedition, you need to inform General Reynolds if there is a problem." Elizabeth answered quietly.

"Well if any of us on the expedition had our way, he won't even be here or he will be gone by the end of the year and you will be back." He answered back. "Anyway he don't trust him, could you please come?" Rodney continued begging. John and Elizabeth leaned back, quickly looked at each other, before looking back at Rodney.

"Elizabeth this is the first time I have heard him beg, maybe we should just honour his request, or he could beg more?" He asked Elizabeth. Elizabeth considered Rodney's request and ignored what John said, even if she did agree with it slightly.

"Okay, but if the General finds out it be your head." Elizabeth answered. She stood up and starting walking towards the door.

"Um, Elizabeth?" Rodney questioned.

"Yes Rodney."

"Maybe you should consider sorting yourself out before coming with me." He answered. Elizabeth was confused; he was delaying this emergency situation he said he had.

"What are you talking about?" Elizabeth stressed, the tension was heard clearly in her voice.

"Well, I don't know about you, but I suppose I like the raffled hair look and the 'I've been thoroughly kissed' lips like any other guy and I'm sure John doesn't mind as he caused the look, but I'm surprised you like the look." Rodney answered with a smug look. Elizabeth couldn't believe what he just said, 'did I really look like I had rolled in the hay with her military commander.' She questioned herself. To answer her question she walked into John bathroom to look in his mirror.

"Oh god!" She muttered, realising that Rodney was right about the way she looked. John heard Elizabeth muttering.

"Great McKay did you have tell her like that?" He questioned, surprised he hadn't realised what she looked like, as he thought she look great.

"Well …I…" Rodney started to answer, but was interrupted again by John.

"I have one night with her McKay, one night, because we were both dumb enough not to do anything about us until the day before she left. Why can't you let me have that one night? Now I have to share her with you!" John said harshly. Rodney looked closely that John and for the first time in a long time thought about what he was going to say.

"John, I'm sorry I hadn't realise." He paused. His apology cause John to look at Rodney in shock, no one would believe him, if he told them what Rodney just said. "I let you in on a little secret, there no emergency." He paused again. John's face turned cold by Rodney's statement. "Hey, wait until I have finished what I was going to say before you kill me. Okay we're giving her a party." Rodney explained, pointing towards the bathroom door.

"Right, I suppose I can't keep her to myself, I suppose I'll share." John muttered, walking towards the bathroom. He wasn't happy about sharing Elizabeth with anyone. "I suppose I clean myself up as well." He continued. He walked into the bathroom and saw Elizabeth with his hair brush trying to make her hair lay flat. She looked towards him and smiled.

"Is it the brush that makes your hair wild? Because it seems to make mine more wild." She questioned, causing John to chuckle.

"No, look Elizabeth they're throwing you a surprise Party, that's the emergency." John told her. He wasn't sure if he should have told her, but he wanted her to be on her guard. She looked at his reflection in the mirror, trying to see if what he was saying was true.

"They are what?" He whispered. "I hate surprises." She continued. John came up behind her and brought his arms around her, hugging her tightly against his body. He looked into her eyes via the mirror and she did the same with him.

"Yeah I know." He whispered in her ear. "You could go out there and tell Rodney you have changed your mind, that you will be staying with me here." He continued and kissed her neck, causing her to moan.

"Sounds like a good idea." She answered, but knew she would still go, knowing now it was a party she had was going to. But was detracted by John as he continually kissed her neck.

"John, we have to go, I have to say good bye." She stated, which caused John to stop kissing her neck and tightened his hold around her waist.

"I don't want to say goodbye." He answered as he buried his head in shoulders.

"John they deserve to say goodbye in their way, even if it is a party, as much as you do." She said softly. She he didn't want to leave his arms, as much as he didn't want to let go, but reality of their situation had finally been reinstalled.

"I know!" He said quietly as he pulled away. "We better get to the party then." He continued. After a few minutes, they had rejoined Rodney in the bedroom and were on their way to the party.

As they walked into the mess hall, she smiled at the decoration and cheers she heard from her expedition members, it brought tears to her eyes.

By the time the party had ended John had only saw Elizabeth from across the room as she made her way round the room, he was slightly disappointed that he hadn't spoken to her since arriving, but knew they still had all night. That much he could clearly see in her eyes, every time their eyes met.

John woke up the morning after the party and noticed Elizabeth was still sleeping, deeply, her body wrapped round his. He eyes quickly flicked to the clock on the wall and realised Elizabeth only had two and a half hours until she was out of his life. He tightened his hold on her; he didn't want to let go, ever. He just wished he found out earlier the way he felt about her, it could have meant they have more time together. He shook his head not understanding there the thought came from, he had never looked back and thought about what he could have done differently. He had always believed what's in the past should stay there; Elizabeth was the first thing to make him look back and wished he could change things.

"Like making sure she would never leave." He muttered softly.

Elizabeth turned towards John; she had woken up when John had pulled her closer, she only pretended sleep, so she could believe the moment could last forever. When she heard him say something, she didn't hear all his words clearer, she only heard 'never leave', which made her smile and realised she couldn't pretend any more; she needed to wake up.

Elizabeth opened her eyes and the first thing she saw was John's eye's staring right into her eyes. Sorrow filled his eyes, which seem to fill right into her soul, after a while the sorrow got so much the dam broke and suddenly she found herself crying and John gathered her closer. Sobs racked her body she didn't want to leave him; the pain of leaving him had suddenly hit her full force and she never felt such emotional pain like this, like her soul was ripping in two.

When Elizabeth started crying he couldn't help, but feel the same, he knew it filled his eyes, which made her to start crying, but he never thought he could feel like this. The harder she cried the more pain he felt, he wondered how anyone could hurt the women he held in his arms so much, the people at Earth didn't realise how asking someone to leave Atlantis that they now considered home, could cause pain. They believe all the people on Atlantis still thought of Earth as home, how wrong could some people be, especially ones that never left their home countries or planet.

Only when they pulled apart from each other a while later did he realise that he had been crying along with her, for one second and only one second, he felt ashamed to cry in front of her, but realised he could be weak in front of her as she was her strength. Looking at the clock again he realised they had to get dressed, somehow one hour had passed since he last looked at the clock. He dropped his arms from around her and immediately her arms went round her body, her body suddenly felling cold. He sat up and turned towards her, she sat up as well. She realised it was time a wake up and meet reality. He quickly gathered her a hug, realising what she was thinking.

"We have to get up!" He stated to her, once he let go of her.

"I know."

"You only have an hour and a half until you leave." He stated again,

"I know."

"And we both need showers." He stated again. She quickly smiled realising where is conversation was going.

"I know." She replied. Trying a sound gloomily and failing miserably.

"So to conserve time I think we should shower together." He stated, while wriggling his eyebrows.

"Well that's a great idea, but I think it's going to waste more time then conserve it."

"Um, I suppose you're right, but it doesn't seem to be a waste of time to me, after all I will have the women I desire the most in the whole galaxy in my arms, naked, with water raining all over her. Believe me the time won't be wasted." He stated, his voice getting huskier the more he spoke. Elizabeth couldn't help, but blush. Even though she had had her fair share of lovers, they were all, only in the bed types, when it came to making love. She had always wondered how it would fill to make love in the showered. Her deepest fantasy was to make love outdoors in the forest, in her the dreams the thrill of getting caught or knowing someone was watching made it more exciting.

John looked at her wondering why she blushed. Only one thing came to mind.

"Elizabeth, you have never shared a shower before have you?" He asked. She thought about his question, she had if you included the gym changing rooms when she was at school, but knew he didn't mean that way, she just shook her head in a negative response. Desire burned in John eyes when she shook her head, he had never been in a relationship where he could show someone the excitement of variety could have in your love life.

"Then Elizabeth we are sharing a shower and when I next come to Earth I can show you more." He stated, pulling her snugly against him and kissing her hungrily.

"Good because I want you to show me."

John dragged her into the shower and Elizabeth couldn't help, but giggle in excitement.

An hour later again having been thoroughly cleaned, they were making there way to the control room, the long way round. Just before they entered the main section of the control room, where the crowd of people were waiting, John pulled her to one side.

"I have something to tell you. Three weeks ago when General O'Neill told me you were leaving, he authorised, no ordered me to take a two week vacation. So I'll back on Earth in two weeks and I was wondering if you could let me stay with you? I can't think of a better place I would rather be." He mumbled, nervous of what she would say and hoping last night wasn't just her way of saying goodbye.

"John." She softly spoke, while reaching up and touching his face. "I would feel insulted if you didn't stay. Earth won't feel like home, unless you are there and I know I have to start thinking of Earth as my home. So you see you have to come and stay, as it won't be home without you. I love you John."

John was relived she said yes and on cloud nine when she said she loved him. He knew last night she felt deeply for him, but wasn't sure if she loved him, it felt great to be in love with her, but awful at the same time, because she was leaving. He cupped her face and pulled her close and kissed her, knowing it was going to be their last for a while.

"I love you, too." He whispered when the kissed ended. He placed his forehead on hers and looked longingly into her eyes.

"As much as I love to keep you here, if we are any longer they will send out a search party." He stated, which cause her to laugh, which ended as a straggled cry, they quickly embraced each other again, before letting go and meeting the rest of the expedition.

Ten minutes later Elizabeth had said her goodbye speech, she was about to step through the Stargate, but she quickly look back and her eyes met John's. She could see the longing, but knew everyone else wouldn't see what she saw, she smile slightly and John raised his hand in a goodbye jester. She told a deep breathe finally able to step through the Stargate.

John watched her struggling to cross the threshold and he hated she had to leave. John stay standing in front of the open Stargate until it disengaged. Only then he left, his whole body feeling numb. His team had stood by him until the last minute and Rodney was about to chase after him, as he wasn't to sure John should be alone, but Ronan had grabbed his arm hard.

"Just leave him McKay he only needs time." Ronan said.

"No he doesn't he needs Elizabeth." Rodney whispered harshly, making sure the new General in charge couldn't hear what he was saying.

"I just hope her leaving will effect him much, but I'm counting my chickens." Rodney answered. He confused Ronan and Teyla with his expressions, but they were getting use to it now. They just thought the Humans from Earth were weird.

After walking through the Stargate the first person Elizabeth saw was General O'Neill. She smiled at him, she had always respect the General and now was one of her closest friends on Earth.

"General it's good to see you." She greeted him.

"Like wise Doctor, but call me Jack and I will call you Elizabeth, Okay?" He asked. He had never really like calling him General all the time since his promotion.

"Sure, we have a deal." She answered as walked down the ramp and into the corridor. Jack was walking her to the infirmary which was the first place anyone went, when they came through the Stargate to Earth.

"So are you glad to be home?" He asked. Elizabeth paused in the corridor and Jack turned round to face her, Jack hated what he saw and that saw sorrow.

"ignore the question Elizabeth, it was a stupid question. I know you have just left your home. I don't think Earth could be home now for quite a few members of your expedition." He stated, knowing she would grateful for the understanding. "I just want you to know, I was always trying to get you to stay the expedition leader. But the politicians think they know best." Elizabeth smiled.

"Jack I know your were always on my side, I don't blame you. But I will have nothing to be with the IOA any more. I will consult sometimes, if they want me here, but not the IOA. Of course if Atlantis needs me, I would drop everything I am doing at the time and run back as fast as I can." She answered.

"Good to know, someone hates the IOA bastards, as well." He stated and she just smiled, no one was like Jack O'Neill, even though John was closest to the General in personality.

End of chapter one.

_**Note: The story was only going to be I one shot, but it's turning into a epic. I haven't even really started the plot line of the story, that I wanted to write, I thought I should start with some background and that is the above chapter.**_

_**Please review, I always welcome any views, so please don't be shy.**_


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